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INSEGT(1) INSEGT(1)

NAME

insegt - INtersecting SEcond Generation sequencing daTa with annotation

SYNOPSIS

insegt [OPTIONS] <ALIGMENTS-FILE> <ANNOTATIONS-FILE>

DESCRIPTION

INSEGT is a tool to analyze alignments of RNA-Seq reads (single-end or paired-end) by using gene-annotations.

Input to INSEGT is a SAM file containing the alignments and a file containing the annotations of the reference genome, either in GFF or GTF format.

REQUIRED ARGUMENTS


Valid filetype is: .sam.

Valid filetypes are: .gtf and .gff.

OPTIONS

Display the help message.
Display version information.

Options: :

Output filename for read-output, which contains the mapped annotations followed by their parent annotation. Valid filetype is: .gff.
Output filename for anno-output, which contains the annotations similar to the GFF input and additionally the counts of the mapped reads and the normalized expression levels in RPKM. Valid filetype is: .gff.
Output filename for tuple-output, which contains exon tuples connected by reads or matepairs. Valid filetype is: .gff.
Output filename for fusion-output, which contains exon tuple of gene fusions (Advanced option, currently no output port for KNIME). One of gff.
ntuple Default: 2.
Offset to short alignment-intervals for search. Default: 5.
Threshold for allowed gaps in alignment (not introns). Default: 5.
Threshold for min. count of tuple for output. Default: 1.
Threshold for min. RPKM of tuple for output. Default: 0.0.
Create only maxTuple (which are spanned by the whole read).
Create only Tuple of exact length n. By default all tuple up to the given length are computed (if -m is set, -e will be ignored).
Orientation of reads is unknown.

EXAMPLES

Run INSEGT on example files with default parameters.
Run INSEGT on example files and only compute maxTuple.
Run INSEGT on example files and only output tuple with a min. count of 2.
insegt 1.1.10 [tarball]